[Bioperl-l] New enzymes for RestrictionEnzyme.pm

[Brian Osborne]

Ryan,

Good. If you don't mind I'll put this into the scripts/contributed directory
under your name, which is for useful scripts which don't use Bioperl.

Brian O.

-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Ryan Brinkman
Sent: Wednesday, August 14, 2002 12:27 PM
To: bioperl-l@bioperl.org; sac@bioperl.org; brian_osborne@cognia.com
Subject: RE: [Bioperl-l] New enzymes for RestrictionEnzyme.pm


This seems to work.

Cheers,
Ryan

#!/usr/bin/perl
# Generate an updated rebase enzyme list

my $strider=@ARGV[0]; #commercial_version_rebase_strider_format

open (FILEIN,$strider) or die "can't open $strider:$!\n";

while (<FILEIN>){
  chomp;
 # print "a:$_\n";
  unless (/#/){
   # print "b\n";
    ($enzyme,$cutsite)=split(',');
  #  print "c:$cutsite\n";
    if ($cutsite =~ m#/#){
  #    print "match $-[0]\n";

      $match=$-[0];
    }
    ($seqfixed=$cutsite) =~ s/\///g;
    $seqfixed=uc $seqfixed;
    #print "s:$seqfixed\n";
    print " \'$enzyme\'\t=> \'".$seqfixed." ".$match."\'\,\n";
  }
}


>>> "Brian Osborne" <brian_osborne@cognia.com> 08/14/02 06:25AM >>>
Ryan and Steve,

Ryan, thank you for pointing this out, we'll update.

Steve C., you mention a converter script, rebase2perl.pl, in
RestrictionEnzyme.pm. Do you know where this is and/or can you send it to
me?

Thanks again,

Brian O.

-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Ryan Brinkman
Sent: Monday, August 12, 2002 8:13 PM
To: bioperl-l@bioperl.org
Cc: sac@bioperl.org
Subject: [Bioperl-l] New enzymes for RestrictionEnzyme.pm


I just had occasion to use  RestrictionEnzyme.pm, and noticed the list may
be out of date (a comment says it was built on a version dated Jan 29 98").
I think the following entries can be added based on my parsing of the latest
version of rebase (Aug 01 2002)

'Acc65I'        => 'GGTACC 1',
 'AceII'        => 'GCTAGC 5',
 'Asp718I'      => 'GGTACC 1',
 'BbeI'         => 'GGCGCC 5',
 'BfrBI'        => 'ATGCAT 3',
 'Bme1580I'     => 'GKGCMC 5',
 'BseBI'        => 'CCWGG 2',
 'BseSI'        => 'GKGCMC 5',
 'BsiLI'        => 'CCWGG 2',
 'Bsp120I'      => 'GGGCCC 1',
 'BssKI'        => 'CCNGG 0',
 'BssNAI'       => 'GTATAC 3',
 'Bst1107I'     => 'GTATAC 3',
 'BstAPI'       => 'GCANNNNNTGC 7',
 'BstKTI'       => 'GATC 3',
 'BstNI'        => 'CCWGG 2',
 'BstOI'        => 'CCWGG 2',
 'BstSCI'       => 'CCNGG 0',
 'Bst2UI'       => 'CCWGG 2',
 'BstZ17I'      => 'GTATAC 3',
 'BthCI'        => 'GCNGC 4',
 'Cfr9I'        => 'CCCGGG 1',
 'ChaI'         => 'GATC 4',
 'Csp6I'        => 'GTAC 1',
 'CviAII'       => 'CATG 1',
 'Ecl136II'     => 'GAGCTC 3',
 'EcoHI'        => 'CCSGG 0',
 'EcoICRI'      => 'GAGCTC 3',
 'EcoT22I'      => 'ATGCAT 5',
 'EgeI'         => 'GGCGCC 3',
 'EheI'         => 'GGCGCC 3',
 'EsaBC3I'      => 'TCGA 2',
 'FatI'         => 'CATG 0',
 'FmuI'         => 'GGNCC 4',
 'FspAI'        => 'RTGCGCAY 4',
 'Hin6I'        => 'GCGC 1',
 'HinP1I'       => 'GCGC 1',
 'Hpy8I'        => 'GTNNAC 3',
 'Hpy99I'       => 'CGWCG 5',
 'Hpy178III'    => 'TCNNGA 2',
 'Hpy188I'      => 'TCNGA 3',
 'Hpy188III'    => 'TCNNGA 2',
 'HpyCH4I'      => 'CATG 3',
 'HspAI'        => 'GCGC 1',
 'KasI'         => 'GGCGCC 1',
 'LpnI'         => 'RGCGCY 3',
 'Mph1103I'     => 'ATGCAT 5',
 'MroNI'        => 'GCCGGC 1',
 'MvaI'         => 'CCWGG 2',
 'NgoAIV'       => 'GCCGGC 1',
 'NgoMIV'       => 'GCCGGC 1',
 'Nli3877I'     => 'CYCGRG 5',
 'NsiI'         => 'ATGCAT 5',
 'OliI'         => 'CACNNNNGTG 5',
 'Ppu10I'       => 'ATGCAT 1',
 'PsiI'         => 'TTATAA 3',
 'Psp03I'       => 'GGWCC 4',
 'PspAI'        => 'CCCGGG 1',
 'PspOMI'       => 'GGGCCC 1',
 'PssI'         => 'RGGNCCY 5',
 'SciI'         => 'CTCGAG 3',
 'SelI'         => 'CGCG 0',
 'SfoI'         => 'GGCGCC 3',
 'Sse232I'      => 'CGCCGGCG 2',
 'TaiI'         => 'ACGT 4',
 'TauI'         => 'GCSGC 4',
 'TscI'         => 'ACGT 4',
 'UnbI'         => 'GGNCC 0',
 'VpaK11AI'     => 'GGWCC 0',
 'XmaI'         => 'CCCGGG 1',
 'XmaCI'        => 'CCCGGG 1',
 'ZraI'         => 'GACGTC 3',
 'Zsp2I'        => 'ATGCAT 5',



Thanks for a great module,
Ryan Brinkman
Xenon Genetics Inc.



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